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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttcctttctgtgattacatgtcattcaatgtcttgaactgagggtacgggttaatgaggccaaaatttgtttcatccaaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGAGAAGTGCTGTTGCTTAGGTGAAAAACTCTGAAAGAACCTCTGTTGATAG

Basic information

species Vitis vinifera
transcript Vv00s0252g00030.t01
intron # 6
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110377578|gb|EC942653.1|EC942653
EST:     GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAG                         GTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
genomic: GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAGgtgaggttcc ... caaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
EST: gi|110700165|gb|EE077889.1|EE077889
EST:     GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAG                         GTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
genomic: GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAGgtgaggttcc ... caaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
EST: gi|110723662|gb|EE101228.1|EE101228
EST:     GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAG                         GTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
genomic: GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAGgtgaggttcc ... caaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
EST: gi|110385058|gb|EC949544.1|EC949544
EST:     GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAG                         GTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
genomic: GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAGgtgaggttcc ... caaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
EST: gi|110724958|gb|EE101251.1|EE101251
EST:     GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTNAAG                         GTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA
genomic: GAAGTTGAAGGCAACTGAACGCCACTCATCATGATGATAATCTGTTAAAGgtgaggttcc ... caaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaactgagggtacgggttaatgaggccaaaatttgtttcatccaaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGAGAAGTGCTGTTGCTTAGGTGAAAAACTCTGAAAGAACCTCTGTTGATAG
                 ggttaat  putative branch site (score: 4)
                                      tttcatcc  putative PPT
                              aaaatttgtttcat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggttcctttctgtgattacatgtcattcaatgtcttgaactgagggtacgggttaatgaggccaaaatttgtttcatccaaattgcagGTGAGTTATAAGCTGAGCATGTAGTCTATGGAATTGGGTTACTATTTGTGAGAAGTGCTGTTGCTTAGGTGAAAAACTCTGAAAGAACCTCTGTTGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC